search

lawremi / ggbio

Grid and ggplot2 based visualization for biological data
111 stars 24 forks source link

Warning message: Ignoring unknown parameters (group.selfish, label, utr.geom) #164

Open ChangqingW opened 2 years ago

ChangqingW commented 2 years ago

When using ggbio::autoplot and geom_alignment on CompressedGRangesList and GRanges, ggplot throw warnings for unknown parameters. (group.selfish for CompressedGRangesList, label, utr.geom for GRanges)

isoform_gff.rds.zip

library(ggbio)
isoform_gff <- readRDS('isoform_gff.rds')
plot_isoforms <- ggbio::autoplot(isoform_gff, label = TRUE) +
  theme_bw() + theme(
    panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
    panel.background = element_blank(), axis.line = element_line(colour = "black")
  )
# Ignoring unknown parameters: group.selfish
plot_isoforms

i <- names(isoform_gff)[2]
p <- ggplot(isoform_gff[[i]]) +
  geom_alignment(
    label = FALSE, range.geom = "rect",
    gap.geom = "arrow", utr.geom = "rect"
  ) +
  xlim(c(min(min(start(isoform_gff))), max(max(end(isoform_gff))))) +
  theme(
    axis.line = element_blank(), axis.text.x = element_blank(),
    axis.text.y = element_blank(), axis.ticks = element_blank(),
    axis.title.x = element_blank(), axis.title.y = element_blank(),
    legend.position = "none", panel.background = element_blank(),
    panel.border = element_blank(), panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(), plot.background = element_blank(),
    plot.margin = margin(20, 0, 20, 0), plot.title = element_text(hjust = 0.5)
  )
 p 
Constructing graphics...
Warning message:
Ignoring unknown parameters: group.selfish 

Warning messages:
1: Ignoring unknown parameters: label, utr.geom 
2: Ignoring unknown parameters: label, utr.geom 
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /stornext/System/data/apps/R/R-4.2.0/lib64/R/lib/libRblas.so
LAPACK: /stornext/System/data/apps/R/R-4.2.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggbio_1.44.0        ggplot2_3.3.6       BiocGenerics_0.42.0

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  reticulate_1.25             RUnit_0.4.32                tidyselect_1.1.2            RSQLite_2.2.14             
  [6] AnnotationDbi_1.58.0        htmlwidgets_1.5.4           grid_4.2.0                  BiocParallel_1.30.3         devtools_2.4.3             
 [11] munsell_0.5.0               ScaledMatrix_1.4.0          codetools_0.2-18            statmod_1.4.36              scran_1.24.0               
 [16] withr_2.5.0                 colorspace_2.0-3            Biobase_2.56.0              filelock_1.0.2              OrganismDbi_1.38.1         
 [21] knitr_1.39                  rstudioapi_0.13             stats4_4.2.0                SingleCellExperiment_1.18.0 labeling_0.4.2             
 [26] MatrixGenerics_1.8.0        rcmdcheck_1.4.0             GenomeInfoDbData_1.2.8      farver_2.1.0                bit64_4.0.5                
 [31] rprojroot_2.0.3             basilisk_1.8.0              vctrs_0.4.1                 generics_0.1.2              xfun_0.31                  
 [36] biovizBase_1.44.0           BiocFileCache_2.4.0         R6_2.5.1                    doParallel_1.0.17           GenomeInfoDb_1.32.2        
 [41] ggbeeswarm_0.6.0            clue_0.3-61                 rsvd_1.0.5                  locfit_1.5-9.5              AnnotationFilter_1.20.0    
 [46] bitops_1.0-7                cachem_1.0.6                reshape_0.8.9               DelayedArray_0.22.0         assertthat_0.2.1           
 [51] BiocIO_1.6.0                scales_1.2.0                nnet_7.3-17                 beeswarm_0.4.0              gtable_0.3.0               
 [56] beachmat_2.12.0             biocViews_1.64.0            processx_3.6.1              ensembldb_2.20.2            rlang_1.0.2                
 [61] GlobalOptions_0.1.2         splines_4.2.0               rtracklayer_1.56.0          lazyeval_0.2.2              dichromat_2.0-0.1          
 [66] checkmate_2.1.0             BiocManager_1.30.18         yaml_2.3.5                  reshape2_1.4.4              GenomicFeatures_1.48.3     
 [71] backports_1.4.1             Hmisc_4.7-0                 RBGL_1.72.0                 tools_4.2.0                 usethis_2.1.6              
 [76] xopen_1.0.0                 ellipsis_0.3.2              RColorBrewer_1.1-3          sessioninfo_1.2.2           Rcpp_1.0.8.3               
 [81] plyr_1.8.7                  base64enc_0.1-3             sparseMatrixStats_1.8.0     progress_1.2.2              zlibbioc_1.42.0            
 [86] purrr_0.3.4                 RCurl_1.98-1.7              ps_1.7.1                    basilisk.utils_1.8.0        prettyunits_1.1.1          
 [91] rpart_4.1.16                viridis_0.6.2               GetoptLong_1.0.5            cowplot_1.1.1               S4Vectors_0.34.0           
 [96] ggrepel_0.9.1               SummarizedExperiment_1.26.1 cluster_2.1.3               fs_1.5.2                    magrittr_2.0.3             
[101] data.table_1.14.2           circlize_0.4.15             ProtGenerics_1.28.0         matrixStats_0.62.0          pkgload_1.2.4              
[106] hms_1.1.1                   XML_3.99-0.10               jpeg_0.1-9                  IRanges_2.30.0              gridExtra_2.3              
[111] shape_1.4.6                 testthat_3.1.4              compiler_4.2.0              biomaRt_2.52.0              scater_1.24.0              
[116] tibble_3.1.7                crayon_1.5.1                htmltools_0.5.2             Formula_1.2-4               tidyr_1.2.0                
[121] DBI_1.1.3                   dbplyr_2.2.0                ComplexHeatmap_2.12.0       rappdirs_0.3.3              Matrix_1.4-1               
[126] brio_1.1.3                  cli_3.3.0                   metapod_1.4.0               parallel_4.2.0              igraph_1.3.2               
[131] GenomicRanges_1.48.0        pkgconfig_2.0.3             GenomicAlignments_1.32.0    dir.expiry_1.4.0            foreign_0.8-82             
[136] scuttle_1.6.2               xml2_1.3.3                  roxygen2_7.2.0              foreach_1.5.2               vipor_0.4.5                
[141] dqrng_0.3.0                 FLAMES_1.3.3                stringdist_0.9.8            XVector_0.36.0              BiocCheck_1.32.0           
[146] stringr_1.4.0               VariantAnnotation_1.42.1    callr_3.7.0                 digest_0.6.29               graph_1.74.0               
[151] Biostrings_2.64.0           htmlTable_2.4.0             edgeR_3.38.1                DelayedMatrixStats_1.18.0   restfulr_0.0.15            
[156] curl_4.3.2                  Rsamtools_2.12.0            rjson_0.2.21                lifecycle_1.0.1             jsonlite_1.8.0             
[161] BiocNeighbors_1.14.0        limma_3.52.2                viridisLite_0.4.0           desc_1.4.1                  BSgenome_1.64.0            
[166] fansi_1.0.3                 pillar_1.7.0                lattice_0.20-45             GGally_2.1.2                KEGGREST_1.36.2            
[171] fastmap_1.1.0               httr_1.4.3                  pkgbuild_1.3.1              survival_3.3-1              glue_1.6.2                 
[176] remotes_2.4.2               png_0.1-7                   iterators_1.0.14            bluster_1.6.0               bit_4.0.4                  
[181] stringi_1.7.6               blob_1.2.3                  BiocSingular_1.12.0         latticeExtra_0.6-29         memoise_2.0.1
ChangqingW commented 2 years ago

seems like ggplot2 is complaining group.selfish being passed to layer